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The detection of B-form/A-form junction in a deoxyribonucleotide duplex
V I Ivanov1, L E Minchenkova, G Burckhardt
1W. A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
Biophysical Journal
|December 1, 1996
Summary
This study shows a deoxyoligonucleotide duplex transitions from B- to A-conformation in trifluorethanol (TFE) solution, forming a B/A junction. Ligand binding confirms this junction, suggesting biological relevance for DNA-protein complexes.
Area of Science:
- Molecular Biology
- Biophysics
- Structural Biology
Background:
- The B- and A-conformations represent distinct structural states of DNA.
- Understanding DNA conformational transitions is crucial for comprehending DNA-protein interactions and biological functions.
Purpose of the Study:
- To investigate the B- to A-conformation transition of a specific deoxyoligonucleotide duplex in varying trifluorethanol (TFE) concentrations.
- To identify and characterize the formation of a B/A junction during this transition.
- To assess the biological relevance of the observed B/A junction.
Main Methods:
- Circular dichroism spectroscopy was employed to monitor conformational changes.
- The effect of TFE concentration on DNA structure was analyzed.
- Distamycin A and netropsin, known B-DNA selective ligands, were used to probe the B/A junction.
Main Results:
- A two-step B- to A-conformation transition was observed with increasing TFE concentration.
- A B/A junction was identified around 73% TFE, with the GC-rich region transitioning first, followed by the AT-rich region.
- Ligand binding experiments confirmed the existence of the B/A junction and demonstrated suppression of A-form formation in the B-philic region.
- The free energy of the B/A junction was estimated at 2.1 kcal/mol.
Conclusions:
- The deoxyoligonucleotide duplex undergoes a distinct B- to A-conformation transition with a stable B/A junction in TFE solutions.
- The findings support the biological relevance of B/A junctions, particularly in the context of DNA-protein complexes like those involving HIV reverse transcriptase.